John Brookfield Ecology Club 11 th February 2010

 Circular DNAs derived from bacterial symbionts  16kb, 37 genes (in humans)  Rapid evolutionary rates in warm blooded vertebrates (particularly in “D loop”)  Maternally transmitted and non-recombining

2Nf

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Nor Nor Nor Nor Sou Sou Sou Sou

Animals from Northern and Southern Populations (complete migration and mixing) Sou Nor Sou Nor Sou Nor Sou Nor

Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou MRCA

 Hardy-Weinberg Formula: q=1-p  AA: p 2  Aa: 2pq  aa: q 2 Random Mating Inbreeding (specified by F ), when homozygotes exceed p 2 +q 2

p=0.8 q=0.2 p=0.2 q=0.8

 F ST =(p 1 -p 2 ) 2 /4(p(1-p))  -scaled squared difference in allele frequency between the populations  -averaged over alleles and loci

p=0.8 q=0.2 p=0.2 q=0.8 F ST = ( ) 2 /(4x0.5x0.5)=0.36

What does F ST mean  F ST =(p 1 -p 2 ) 2 /4(p(1-p)) =( ) 2 /(4x0.5X0.5)=0.36 How many heterozygotes expected (Hardy- Weinberg)=2p(1-p)=0.50 How many seen= 2p 1 (1-p 1 )/2 +2p 2 (1-p 2 )/2 =0.8x x0.8 =0.32

p=0.9 q=0.1 p=0.1 q=0.9 F ST = ( ) 2 /(4x0.5x0.5)=0.64

p=1.0 q=0.0 p=0.0 q=1.0 F ST = ( ) 2 /(4x0.5x0.5)=1.00

p=0.6 q=0.4 p=0.4 q=0.6 F ST = ( ) 2 /(4x0.5x0.5)=0.04

pA=0.6 qa=0.4 pB=0.7 qb=0.3 pA=0.4 qa=0.6 pB=0.3 qb=0.7 Linkage Disequilibrium: Association of A and B and association of a and b

The Island Model: F ST =1/(1+4N e m)

Isolation By Distance

PopulationsBCDE A B C D0.0634

PopulationsBCDE A B C D3.69

PopulationsBCDE A B C D0.0634

 AMOVA-Laurent Excoffier ARLEQUIN   Designed for mtDNAs initially  Takes various levels-populations and subpopulations, etc. molecular variation between them as a proportion of total molecular variance

Methods-Nested Clade Analysis (1) Templeton, A. (2006) Population genetics and microevolutionary theory. Wiley

 D c : Clade distance: Geographical separation of individuals within a clade  D n : Nested clade distance: Distance from the centre of a clade and the mean location of individuals in related clades (all those within the same higher level of nesting)  Isolation by distance: A clade-defining mutation arises in a single location, and its spread will increase with age. Clades within that clade (nested clades) will have a geographic distribution within that of the ancestral clade.  Fragmentation: Strict correlation of clades with geography- which breaks down as older clades are considered.  Range Expansion: Subclades can be more widespread geographically than their ancestral clades.

 Samples individuals and genotypes at many loci  Creates subpopulations where there are Hardy-Weinberg proportions and linkage equilibrium within subpopulations  Assigns individuals to subpopulations  Methods: STRUCTURE - Jonathan Pritchard

 G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, ,  k/~gigu/Geneland/ k/~gigu/Geneland/ Methods-GENELAND

 Selective Sweeps  Complete or partial  Locus-specific

Natural Selection  Effects on F ST ◦ Balanced polymorphism throughout species range gives low F ST ◦ Geographically localised selection gives high F ST